Ecosyste.ms: Papers

10.3389/fninf.2021.561689

QDECR: A Flexible, Extensible Vertex-Wise Analysis Framework in R
Cited by: 13
Author(s): Sander Lamballais, Ryan L. Muetzel
Software Mentions: 9
Published: over 3 years ago

10.1186/s13059-020-02067-3

Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II, and Pol III
Cited by: 81
Author(s): Yongpeng Jiang, Jinfeng Huang, Kehuan Lun, Boyuan Li, Haonan Zheng, Yuanjun Li, Rong Zhou, Duan Wenjia, Chenlu Wang, Yuanqing Feng, Huilu Yao, Cheng Li, Ji Xiong
Software Mentions: 5
Published: over 4 years ago

10.1186/s12859-020-03725-w

Seagull: lasso, group lasso and sparse-group lasso regularization for linear regression models via proximal gradient descent
Cited by: 15
Author(s): Jan Klosa, Noah Simon, Pål O. Westermark, Volkmar Liebscher, Dörte Wittenburg
Software Mentions: 5
Published: over 4 years ago

10.1098/rspb.2019.2253

Lens transmittance shapes ultraviolet sensitivity in the eyes of frogs from diverse ecological and phylogenetic backgrounds
Cited by: 14
Author(s): Carola A. M. Yovanovich, Michele E. R. Pierotti, Almut Kelber, Gabriel Jorgewich-Cohen, Roberto Ibáñez, Taran Grant
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0236540

Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes
Cited by: 38
Author(s): Beverly McClenaghan, Nicole A Fahner, David Côté, Julek Chawarski, Avery McCarthy, Hoda Rajabi, Gregory A. C. Singer, Mehrdad Hajibabaei
Software Mentions: 4
Published: about 4 years ago

10.1038/s41597-019-0174-7

Creating reproducible pharmacogenomic analysis pipelines
Cited by: 5
Author(s): Anthony Mammoliti, Alexander Smirnov, Zhaleh Safikhani, Wail Ba-Alawi, Benjamin Haibe‐Kains
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0231574

Genetic diversity and connectivity of Flaccisagitta enflata (Chaetognatha: Sagittidae) in the tropical Atlantic ocean (northeastern Brazil)
Cited by: 6
Author(s): Danielle C M Melo, Simone Maria de Albuquerque Lira, Ana Paula B. Moreira, Lucas Freitas, Camilla A D Lima, Fabiano L. Thompson, Arnaud Bertrand, Alex C. Silva, Sigrid Neumann‐Leitão
Software Mentions: 3
Published: over 4 years ago

10.1128/mSphere.00454-21

A Novel Phage Infecting <i>Alteromonas</i> Represents a Distinct Group of Siphophages Infecting Diverse Aquatic Copiotrophs
Cited by: 16
Author(s): Ruijie Ma, Jiayong Lai, Xiaowei Chen, Long Wang, Yue Yang, Shuzhen Wei, Nianzhi Jiao, Rui Zhang
Software Mentions: 3
Published: over 3 years ago

10.1002/ece3.7443

Qualitative and quantitative methods show stability in patterns of <i>Cepaea nemoralis</i> shell polymorphism in the Pyrenees over five decades
Cited by: 3
Author(s): Daniel Ramos Gonzalez, Angus Davison
Software Mentions: 3
Published: almost 4 years ago

10.1039/c7sc04531j

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields
Cited by: 183
Author(s): Louis Lagardère, Luc‐Henri Jolly, Filippo Lipparini, Félix Aviat, Benjamin Stamm, Zhifeng Jing, Matthew Harger, Hedieh Torabifard, G. Andrés Cisneros, Michael J. Schnieders, Nohad Gresh, Yvon Maday, Pengyu Ren, Jay W. Ponder, Jean‐Philip Piquemal
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12859-020-03726-9

IonCRAM: a reference-based compression tool for ion torrent sequence files
Cited by: 2
Author(s): Moustafa Shokrof, Mohamed Abouelhoda
Software Mentions: 3
Published: over 4 years ago

10.1100/2012/612048

Seasonality of Tropical Instability Waves and Its Feedback to the Seasonal Cycle in the Tropical Eastern Pacific
Cited by: 13
Author(s): Seul Hee Im, Soon Il An, Matthieu Lengaigne, Yign Noh
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12911-016-0376-2

Open data models for smart health interconnected applications: the example of openEHR
Cited by: 17
Author(s): Hans Demski, Sebastian Garde, Claudia Hildebrand
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0059954

Benthic-Pelagic Coupling: Effects on Nematode Communities along Southern European Continental Margins
Cited by: 25
Author(s): Ellen Pape, Daniel O. B. Jones, Elena Manini, Tania Nara Bezerra, Ann Vanreusel
Software Mentions: 2
Published: over 11 years ago

10.1111/eva.12055

Spatiotemporal SNP analysis reveals pronounced biocomplexity at the northern range margin of<scp>A</scp>tlantic cod<i><scp>G</scp>adus morhua</i>
Cited by: 96
Author(s): Nina Overgaard Therkildsen, Jakob Hemmer‐Hansen, Rasmus Hedeholm, Mary S. Wisz, Christophe Pampoulie, Dorte Meldrup, Sara Bonanomi, Anja Retzel, Steffen M. Olsen, Einar Eg Nielsen
Software Mentions: 2
Published: almost 12 years ago

10.5194/gmd-12-3071-2019

Simulating lightning NO production in CMAQv5.2: evolution of scientific updates
Cited by: 19
Author(s): Daiwen Kang, Kenneth Pickering, D. J. Allen, Kristen M. Foley, David C. Wong, Rohit Mathur, Shawn J. Roselle
Software Mentions: 2
Published: over 5 years ago

10.1002/acm2.12363

Applying three different methods of measuring <i>CTDI</i> _{<i>free air</i>} to the extended CTDI formalism for wide-beam scanners (IEC 60601-2-44): A comparative study
Cited by: 6
Author(s): Robert Bujila, Love Kull, Mats Danielsson, Jonas Andersson
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-71563-0

Ocean model resolution dependence of Caribbean sea-level projections
Cited by: 12
Author(s): René M. van Westen, Henk A. Dijkstra, Carine G. van der Boog, Caroline A. Katsman, Rebecca K. James, Tjeerd J. Bouma, Olga Kleptsova, R. Klees, Riccardo Riva, Cornelis Slobbe, Marcel Zijlema, Julie D. Pietrzak
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-021-95482-w

Multi-qubit correction for quantum annealers
Cited by: 12
Author(s): Ramin Ayanzadeh, John E. Dorband, M. Halem, Tim Finin
Software Mentions: 2
Published: over 3 years ago

10.2196/20239

Development of an openEHR Template for COVID-19 Based on Clinical Guidelines
Cited by: 21
Author(s): Mengyang Li, H.A. Leslie, Bin Qi, Shan Nan, Hongshuo Feng, Hailing Cai, Xudong Lü, Huilong Duan
Software Mentions: 2
Published: over 4 years ago

10.1186/s12983-017-0248-3

Different feeding strategies in Antarctic scavenging amphipods and their implications for colonisation success in times of retreating glaciers
Cited by: 13
Author(s): Meike Anna Seefeldt, Gabriela Laura Campana, Dolores Deregibus, María Liliana Quartino, Doris Abele, Ralph Tollrian, Christoph Held
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0103195

Diversity and Distribution of Deep-Sea Shrimps in the Ross Sea Region of Antarctica
Cited by: 28
Author(s): Zeenatul Basher, David A. Bowden, Mark J. Costello
Software Mentions: 1
Published: over 10 years ago

10.1186/s13059-021-02299-x

Promoting reproducibility with Code Ocean
Cited by: 6
Author(s): Barbara Cheifet
Software Mentions: 1
Published: almost 4 years ago

10.2196/24382

Using Information Technology to Assess Patient Risk Factors in Primary Care Clinics: Pragmatic Evaluation
Cited by: 3
Author(s): Leanne Kosowan, Alan Katz, Gayle Halas, Lisa LaBine, Alexander Singer
Software Mentions: 1
Published: almost 4 years ago

10.1093/icesjms/fsaa227

Strengthening the global network for sharing of marine biological collections: recommendations for a new agreement for biodiversity beyond national jurisdiction
Cited by: 7
Author(s): Jane Eva Collins, Muriel Rabone, Thomas Vanagt, Diva J. Amon, Judith Gobin, Isabelle Huys
Software Mentions: 1
Published: about 4 years ago

10.1120/jacmp.v15i5.4901

Evaluation of gantry rotation overrun in axial CT scanning
Cited by: 6
Author(s): Atsushi Fukuda, Pei‐Jan Paul Lin, Kosuke Matsubara, Tosiaki Miyati
Software Mentions: 1
Published: over 10 years ago

10.1120/jacmp.v15i1.4517

Measurement of gantry rotation time in modern ct
Cited by: 10
Author(s): Atsushi Fukuda, Pei‐Jan Paul Lin, Kosuke Matsubara, Tosiaki Miyati
Software Mentions: 1
Published: almost 11 years ago

10.3390/ijerph120201069

Delineating Biophysical Environments of the Sunda Banda Seascape, Indonesia
Cited by: 15
Author(s): Mingshu Wang, Gabby N. Ahmadia, Iliana Chollett, Charles Huang, Helen E. Fox, Anton Wijonarno, Marguerite Madden
Software Mentions: 1
Published: almost 10 years ago

10.1002/acm2.12670

Assessment of longitudinal beam property and contrast uniformity for 256‐ and 320‐row area detector computed tomography scanners in the 160‐mm nonhelical volume‐acquisition mode
Cited by: 6
Author(s): Takanori Hara, Shin‐Ichi Niwa, Atsushi Urikura, Kosuke Matsubara, Takashi Hoshino, Eiji Nishimaru, Tetsuo Taniguchi
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0086130

Impacts of Climate-Change-Driven Sea Level Rise on Intertidal Rocky Reef Habitats Will Be Variable and Site Specific
Cited by: 17
Author(s): Jaqueline Thorner, Lalit Kumar, Stephen Smith
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pbio.1001947

The Common Oceanographer: Crowdsourcing the Collection of Oceanographic Data
Cited by: 35
Author(s): Federico M. Lauro, Svend Jacob Senstius, Jay T. Cullen, Russell Y. Neches, Rachelle M. Jensen, Mark V. Brown, Aaron E. Darling, Michael Givskov, Diane McDougald, Ron Hoeke, Martin Ostrowski, Gayle K. Philip, Ian T. Paulsen, Joseph J. Grzymski
Software Mentions: 1
Published: over 10 years ago

10.1038/srep37180

Overlooked Role of Mesoscale Winds in Powering Ocean Diapycnal Mixing
Cited by: 4
Author(s): Zhao Jing, Lixin Wu, Xiaoyan Ma, Ping Chang
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-017-00593-y

A peculiar lens-shaped structure observed in the South China Sea
Cited by: 11
Author(s): Hongyang Lin, Jianyu Hu, Zhiyu Liu, Igor M. Belkin, Zhenyu Sun, Jia Zhu
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-34786-w

Applicability of Dynamic Energy Budget (DEB) models across steep environmental gradients
Cited by: 24
Author(s): Cristián J. Monaco, Christopher D. McQuaid
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-64580-6

Elevated primary productivity triggered by mixing in the quasi-cul-de-sac Taiwan Strait during the NE monsoon
Cited by: 7
Author(s): Ting-Hsuan Huang, Chen‐Tung Arthur Chen, Yan Bai, Xianqiang He
Software Mentions: 1
Published: over 4 years ago

10.3390/nu12040894

Exploring the Perceptions of Women from Under-Resourced South African Communities about Participating in a Low-Carbohydrate High-Fat Nutrition and Health Education Program: A Qualitative Focus Group Study
Cited by: 3
Author(s): Georgina Pujol-Busquets, James Smith, Kate Larmuth, Sergi Fàbregues, Anna Bach-Faig
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-020-73890-8

Estimating soil water retention for wide ranges of pressure head and bulk density based on a fractional bulk density concept
Cited by: 6
Author(s): Huihui Sun, Jae‐Hoon Lee, Xijuan Chen, Jie Zhuang
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-020-77315-4

Electronic structure with direct diagonalization on a D-wave quantum annealer
Cited by: 18
Author(s): Alexander Teplukhin, Brian K. Kendrick, Sergei Tretiak, Pavel A. Dub
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-021-82197-1

Adaptive hyperparameter updating for training restricted Boltzmann machines on quantum annealers
Cited by: 5
Author(s): Guanglei Xu, William S. Oates
Software Mentions: 1
Published: almost 4 years ago

10.1007/s10943-017-0397-x

“No More Buzz”: A Qualitative Study of the Current Response to HIV in the Anglican Church in the Western Cape, South Africa
Cited by: 1
Author(s): Simon Hallonsten
Software Mentions: 1
Published: over 7 years ago

10.1186/s40814-019-0501-y

A virtual reality intervention for fear of movement for Veterans with chronic pain: protocol for a feasibility study
Cited by: 11
Author(s): Christopher A. Fowler, Lisa Ballistrea, Kerry E Mazzone, Aaron M. Martin, Howard Kaplan, Kevin E. Kip, Jennifer L. Murphy, Sandra Winkler
Software Mentions: 1
Published: about 5 years ago

10.3390/s120100373

Marine Vehicle Sensor Network Architecture and Protocol Designs for Ocean Observation
Cited by: 18
Author(s): Shaowei Zhang, Jiancheng Yu, Aiqun Zhang, Lüxi Yang, Yeqiang Shu
Software Mentions: 1
Published: almost 13 years ago

10.3390/s19030702

A Survey on Unmanned Surface Vehicles for Disaster Robotics: Main Challenges and Directions
Cited by: 92
Author(s): Vitor A. M. Jorge, Roger Granada, Renan G. Maidana, Darlan A. Jurak, Guilherme Heck, Alvaro Negreiros, Davi Henrique dos Santos, Luiz Marcos Garcia Gonçalves, Alexandre M. Amory
Software Mentions: 1
Published: almost 6 years ago

10.3390/s20185374

A Visual Tracker Offering More Solutions
Cited by: 2
Author(s): Long Zhao, Mubarak Adam Ishag Mahmoud, Hongxiang Ren, Meng Zhu
Software Mentions: 1
Published: over 4 years ago

10.3390/s21030831

Affimer-Based Europium Chelates Allow Sensitive Optical Biosensing in a Range of Human Disease Biomarkers
Cited by: 8
Author(s): Eiman Al-Enezi, Alexander Vakurov, Amy Eades, Mingyu Ding, Gin Jose, Sikha Saha, Paul A. Millner
Software Mentions: 1
Published: almost 4 years ago

10.3390/s21051675

Communication Planning for Cooperative Terrain-Based Underwater Localization
Cited by: 5
Author(s): Jacob Anderson, Geoffrey A. Hollinger
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12875-021-01443-7

Patient perspectives on tablet-based technology to collect risk factor information in primary care
Cited by: 1
Author(s): Leanne Kosowan, Alan Katz, Gayle Halas, Alexander Singer
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0241624

The impact of integrating electronic referral within a musculoskeletal model of care on wait time to receive orthopedic care in Ontario
Cited by: 0
Author(s): Heba Tallah Mohammed, Lori-Anne Payson, Mohamed Alarakhia
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0045309

Microbial Distribution and Abundance in the Digestive System of Five Shipworm Species (Bivalvia: Teredinidae)
Cited by: 49
Author(s): Meghan A. Betcher, Jennifer M. Fung, Andrew Han, Roberta M. O’Connor, Romell A. Seronay, Gisela P. Concepción, Daniel L. Distel, Margo G. Haygood
Software Mentions: 1
Published: over 12 years ago

10.3390/e22090953

A Note on the Reproducibility of Chaos Simulation
Cited by: 8
Author(s): Thalita E. Nazaré, Erivelton G. Nepomuceno, Samir A. M. Martins, Denis N. Butusov
Software Mentions: 1
Published: over 4 years ago

10.3390/jimaging5100079

A Contrast-Guided Approach for the Enhancement of Low-Lighting Underwater Images
Cited by: 26
Author(s): Tunai Porto Marques, Alexandra Branzan Albu, Maia Hoeberechts
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0154887

Underwater Optics in Sub-Antarctic and Antarctic Coastal Ecosystems
Cited by: 19
Author(s): Pirjo Huovinen, Jaime Ramírez, Iván Gómez
Software Mentions: 1
Published: over 8 years ago

10.3389/fpls.2020.00789

New Food Crop Domestication in the Age of Gene Editing: Genetic, Agronomic and Cultural Change Remain Co-evolutionarily Entangled
Cited by: 47
Author(s): David L. Van Tassel, Omar Tesdell, Brandon Schlautman, Matthew J. Rubin, Lee R. DeHaan, Timothy E. Crews, Aubrey Streit Krug
Software Mentions: 1
Published: over 4 years ago